Whilst the West Indian merchants could cause their flag officer many headaches with their demands, Rainier was in a different position from that of any other commander-in-chief in that the East India Company was such an important organisation, both in London and on station. It was a key element of the City with its demand for money through bonds and loans, and, at other times, as a provider of finance, men and materials for the government. The Chairman of the Board of Control, which oversaw the activities of the Company on behalf of the government, was headed by Dundas, arguably the second most powerful man in the government and the main director of the war against France. The Company had an army of 192,000 men by 1805 and it had its own fully serviced dry dock at Bombay. This organisation, with so much power and influence both in Britain and abroad, presented an unparalleled challenge to the East Indies flag officer.

Its Governor General was the most important individual in India with whom Rainier had to work: serious conflict between the two would almost certainly have led to failure for Rainier. He needed to manage his relationships with the various bodies within the Company and ensure its officers felt he was working with them, without damaging the goals set for him by the Admiralty. For many people it was difficult to see where the Company ended and the ‘Crown’ began. Indeed, Captain Lennon notes in his Journal that the admiral had great difficulty trying to explain to a native prince the difference between the Company and the King, made worse by an understandable poor command of English on the part of the prince.